Some formats are very particular about frame size. It's built in. Nothing you can do about it except follow the advice to always use the presets for AE comps unless you know exactly what you are doing. Your vertical file is a non standard FLV file size. Simple as that.
As Rick suggests, FLV is very seldom the right choice for exporting. Do you have a specific need for an FLV file?
Most vertical movies are used in digital signage applications. Yours?
The manual for the software that runs the signage should have specific workflow guidelines for producers.